ABSTRACT
Justicieae is the most taxonomically complex tribe in Acanthaceae. Here, we sequenced the plastome of Ecbolium viride, a medicinally important species. The genome was analyzed with previously reported plastome of Justiceae. The plastome of E. viride has quadripartite structure with a length of 151 185 bp. The comparative genomic analyses revealed no structural inversion in Justiceae and some regions (rpoC2, ycf2, ycf1, ndhH rps16-trnQ-UGG, and trnL-CAA-ycf15) exhibiting a significant level of nucleotide divergence. The positive selection analyses revealed that some species in the tribe have undergone adaptive evolution. The visualization of the boundaries between the single copy and inverted repeat regions revealed that Justiceae chloroplast genome experienced some levels of variation, which give an insight into the evolution of the species. The longest genome was in the earliest diverged taxa of the tribe Pseuderanthemum haikangense and from this genome, a series of contraction and expansion occurred contributing to the evolution of other lineages. The plastome-based phylogeny revealed and confirmed the monophyly of Justiceae, polyphyly of Justicia and supported the tribal classification Graptophyllinae, Tetrameriinae, and Isoglossinae. We proposed that Declipterinae should be treated as subtribe and the status of Justiciinae can only be confirmed after the resolution of the polyphyletic Justicia.
ABSTRACT
Hypoestes forskaolii is one of the most important species of the family Acanthaceae, known for its high economic and medicinal importance. It is well distributed in the Arab region as well as on the African continent. Previous studies on ethnomedicine have reported that H. forskaolii has an anti-parasitic effect as well as antimalarial and anthelmintic activities. Previous studies mainly focused on the ethnomedicinal properties, hence, there is no information on the genomic architecture and phylogenetic positions of the species within the tribe Justiceae. The tribe Justicieae is the most taxonomically difficult taxon in Acanthoideae due to its unresolved infratribal classification. Therefore, by sequencing the complete chloroplast genome (cp genome) of H. forskaolii, we explored the evolutionary patterns of the cp genome and reconstructed the phylogeny of Justiceae. The cp genome is quadripartite and circular in structure and has a length of 151,142 bp. There are 130 genes (86 coding for protein, 36 coding for tRNA and 8 coding for rRNA) present in the plastome. Analyses of long repeats showed only three types of repeats: forward, palindromic and reverse were present in the genome. Microsatellites analysis revealed 134 microsatellites in the cp genome with mononucleotides having the highest frequency. Comparative analyses within Justiceae showed that genomes structure and gene contents were highly conserved but there is a slight distinction in the location of the genes in the inverted repeat and single copy junctions. Additionally, it was discovered that the cp genome includes variable hotspots that can be utilized as DNA barcodes and tools for determining evolutionary relationships in the Justiceae. These regions include: atpH-atpI, trnK-rps16, atpB-rbcL, trnT-trnL, psbI-trnS, matK, trnH-psbA, and ndhD. The Bayesian inference phylogenetic tree showed that H. forskaolii is a sister to the Dicliptra clade and belongs to Diclipterinae. The result also confirms the polyphyly of Justicia and inclusion of Diclipterinae within justicioid. This research has revealed the phylogenetic position of H. forskaolii and also reported the resources that can be used for evolutionary and phylogenetic studies of the species and the Justicieae.
Subject(s)
Acanthaceae , Genome, Chloroplast , Phylogeny , Bayes Theorem , Acanthaceae/genetics , GenomicsABSTRACT
The genus Mentha encompasses mint species cultivated for their essential oils, which are formulated into a vast array of consumer products. However, the systematics of the genus Mentha is very complicated and still uncertain. This is largely because of the presence of frequent interspecific hybridization, variation in chromosome number, cytomixis, polymorphism in morphology and essential oil composition under different environmental conditions, colonial mutant propagation, as well as the occurrence of polyploidy, aneuploidy, and nothomorphs. Here, we present the plastome assemblies for a wilt-resistant Saudi Arabian accession of Mentha longifolia (L.) Huds and an alien hybrid Mentha × verticillata L. which are 152,078 bp and 152,026 bp in length, respectively, and exhibited large single-copy (LSC) and small single-copy (SSC) regions separated by a pair of inverted repeat regions. The chloroplast genome of M. longifolia has 133 annotated genes, including 88 protein-coding genes and 37 tRNAs while M. × verticillata has 133 annotated genes, including 87 protein-coding genes and 38 tRNAs. Both cp genomes have eight rRNA genes. Phylogenetic analysis using a total chloroplast genome DNA sequence of 17 species revealed that M. longifolia sequenced in this study did not form a sister relationship with M. longifolia from another study. This opens a window for further investigations.
